# All Questions

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### Algorithm to compute the intersection of meshlines with a boundary

I need a program or an algorithm that computes the intersection of a mesh and a boundary. The mesh is structured orthogonal in nature and the boundary is a circle (for example). This will be used ...
533 views

### How much should scientific software be optimized?

For applications requiring significant computational resources, high performance can be a critical factor when it comes to delivering scientific results or achieving "break-throughs" in reasonable ...
3k views

### How to construct a prolongation and restriction operator for an algebraic multigrid solver?

I am trying to solve a linear system of equations that is sparse, but lacks any kind of banded structure. I have heard that there is a way to extend the principles of a multigrid solver for implicit ...
917 views

### Which linear algebra texts should I read before learning numerical linear algebra?

Assuming one wishes to study numerical linear algebra in depth (and follow journals on numerical linear algebra and matrix theory), which would be a better course/better book to take up at first: ...
864 views

### Sparse hermitian eigensystems: are there better techniques than Arpack or TRLan?

As a part of other work I need to solve relatively large (~1E5x1E5) and sparse (~100 non-zero elements in each raw in few blocks) hermitian eigensystems. Usually only few eigenvalues+vectors are ...
3k views

### High Order derivatives of splines using SciPy

I have created a spline to fit my data in python using: spline=scipy.interpolate.UnivariateSpline(energy, fpp, k=4) The equation I want to use involves a ...
801 views

### Which journals should I read to keep up on advances in solving PDEs numerically?

I solve a lot of PDEs numerically, but applied math isn't my field. I haven't picked up on which applied math journals I should read to keep up with recent developments in the field. What are good ...
359 views

### Open-access journals in Computational Science

In light of the recent petition to boycott Elsevier, I was wondering what options we have in Computational Science for Journals which are completely open-access, Journals which allow/support open-...
594 views

### When analyzing a parallel algorithm, how do you take communication costs into account?

My question is related in spirit to "Is algorithmic analysis by flop counting obsolete?". Counting the number of computational operations in an algorithm is commonly used as a first-order model to ...
356 views

### Pauli repulsion contribution in electronic structure computations

I am looking for a method to estimate the contribution from Pauli repulsion to the interaction energy of a molecular dimer in an electronic structure computation (e.g. with Density Functional Theory). ...
183 views

### Texture analysis methods modern survey paper

I want to study the methods of analyzing textured images. So i searched google scholor but only found very old papers statistical and structural approaches to texture 1979 haralick Image Texture ...
126 views

### Using an approximation algorithm to adapt parameter values of a given algorithm

Problem: I have an incremental online clustering algorithm which need 4 parameters that should be specified by the user before execution. The algorithm will gives "good results" if "a good parameter ...
172 views

### What mapping strategy should I use when solving many large linear systems of equations?

I am working on a problem that involves solving many (thousands) of distinct linear systems of equations, each with thousands of variables. Let's assume that the size of each matrix is exactly the ...
286 views

### How does one handle the source term in the Shallow Water Equations when using the discontinuous galerkin method? [closed]

I use the discontinuous galerkin method to solve the steady flow 1D shallow water equations with a bump at the bottom. This flow is frictionless. I use the runge-kutta method to approximate the time ...
681 views

### Diffusion kernel “guide”

Diffusion kernels are kernels which "project" information about graphs into $R^n$ so that certain machine learning techniques can be performed. I have read through this paper and feel fairly ...
174 views

### Conjugate Gradient with Hierarchical Basis Functions: How can the hierarchical base be decomposed?

I'm trying to implement a Conjugate Gradient solver using Hierarchical Basis Functions, following this paper. In section 3 the paper says that the hierarchical basis matrix $S$ can be decomposed into ...
484 views

### Implementing a fair scheduling policy on Maui/Torque

We have Maui and Torque on our lab's UNIX cluster. Right now, all jobs are served by FIFO. We'd like to implement a more fair policy, but I have not successfully implemented it. The online ...
12k views

2k views

### Two-chordless cycle extraction from a failed comparability graph recognition

I have implemented a comparability graph recognition algorithm from M.C. Golumbic's "Algorithmic graph theory and perfect graphs" book. It is hinted in Fekete, Schepers, and van der Veen's "Exact ...
172 views

### How can I set different axes for different plots in gnuplot?

I want to plot a few sets of data points on the same x-axis that have different units. How can I set different axes for each incompatible quantity?
1k views

### How do I compute the parallel overhead of a parallel code run on a single processor when no sequential code is available?

I'm profiling the performance of PETSc's linear solvers. As I understand it, $$\text{speedup}=\frac{\text{Sequential Time}}{\text{Parallel Time}}.$$ I know that running the parallel code on one ...
3k views

### When do orthogonal transformations outperform Gaussian elimination?

As we know, orthogonal transformations methods (Givens rotations and Housholder reflections) for systems of linear equations are more expensive than Gaussian elimination, but theoretically have nicer ...
2k views

### How can wavelets be applied to PDE?

I would like to learn how wavelet methods can be applied to PDE, but unfortunately I do not know a good resource to learn about this topic. It seems that many introductions to wavelets focus on ...
3k views

### What's the most efficient way to compute the eigenvector of a dense matrix corresponding to the eigenvalue of largest magnitude?

I have a dense real symmetric square matrix. The dimension is about 1000x1000. I need to compute the first principal component and wonder what the best algorithm to do this might be. It seems that ...
6k views

### What are the main differences between PETSc and Trilinos?

As far as I can tell, the two big generic US Department of Energy computational science software frameworks are PETSc and Trilinos. They seem similar at first glance, beyond differences in language (...
197 views

### Can BFGS be used to minimise several functions at once?

I have multiple objective functions which are related to several parameters. I want to minimise more than one objective functions using several parameters. Is it even possible using BFGS? When I used ...
1k views

### How to measure the overall performance of a PETSc program using the -log_summary flag?

When I run a PETSc example in parallel with the flag "-log_summary", the first two tables of information look something like this: ...
279 views

### Approximately “solving” a linear system of equations without a feasible solution

A linear system of equations has the form $Ax = b$, where a matrix $A$ and a vector $b$ are given, and I wish to find a solution vector $x$. Suppose that the system $Ax = b$ has no feasible solution. ...
436 views

### How effective is the 'tendrils of knowledge' approach to Comp. Sci?

I was reading this on Math SE. The basic question is : Assume that someone wishes to study something advanced; one way to do this would be to start off from basics and build up. But the "bigger ...
I have an application in which I am computing a quantity which is approximated by an average over $M$ points. In theory, the average converges to the correct quantity when $M$ is infinite. In practice,...